HALE O'MANA'O RESEARCH

The main goal of our Public Health research is to understand how scientific processes are responsible for producing the interactions and measurements we observe. We use a combination of approaches and technologies that we have developed for use in our studies. Learn more about our research and areas of study below.

RESEARCH

2009-present

BIOINFORMATICS

We still have only a very limited understanding of most aspects about how viral pathogens interact to cause disease.. Answering questions about this is essential for understanding the mechanistic role it plays on other scientific processes, and for developing tools to further explore this research avenue with more sensitive measurements and improved data collection.

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2017-present

PATHOGEN-ASSOCIATED AUTOIMMUNE DISEASE PREVENTION

In an effort to gain a better understanding of the world around us, we have recently begun to use a in depth epitope analysis to investigate the organization and functionality of the diverse parts of our disease model. We are currently looking to expand this work by collaborating with other labs who have the facilities and prior experience to investigate this project further.

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2009-present

EMERGING PATHOGENS

The battle against emerging pathogens is an ongoing, continuous project. We have worked in genomics of Filoviruses (Ebolavirus, Marburgvirus, Cuevavirus), neglected tropical diseases, and more recently, Zika virus and its neurotropism. We are currently working on a project investigating the possibility of emergence of Filoviridae in the New World. collaboration with laboratories and funding towards completing this project is essential.

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2017-present

EMERGENCE OF FILOVIRIDAE IN THE NEW WORLD

It goes without saying that infection by Filoviridae is without a doubt the most lethal of all viral hemorrhagic fevers. The most recent outbreak in West Africa from 2013 to 2015 with over 11,000 deaths and the subsequent extraordinarily severe social economic consequences would bear witness to that. To date all emergence of both of Ebola virus and Marburg virus have occurred only in the continent of Equatorial Africa. The genomic fragments of Ebola Zaire in several species of bat is intriguing. Ebola is a -sense RNA virus, so how could these fragments (both + sense and -sense) have been integrated into bat DNA? The purpose of this initial project is towards the investigation for further field research into the possible emergence of Filoviridae in North and South America.

OUTBREAK NEWS-US

OUTBREAK NEWS-WORLDWIDE

PUBLIC HEALTH INFORMATION AND ANALYTICS-OKLAHOMA

PROJECTS AND PUBLISHED WORK

COMPUTATIONAL EVIDENCE FOR A VIRAL ENCODED MIRNA IN THE INTERGENIC, UNTRANSLATED REGION OF THE ZAIRE EBOLAVIRUS NUCLEOPROTEIN GENE MAY EXPLAIN ITS DIFFERENTIAL VIRULENCE: A POTENTIAL PANDORA ELEMENT

May 3, 2014

Abstract

Ebolavirus is one of the most virulent of human viral pathogens, killing 25-90% of patients within 6-16 days (EBOV and SUDV) resulting from complete disruption of the host immune response. Despite the relatively minor genetic differences between the species, the case fatality rate (CFR) is significantly different. The Zaire Ebolavirus (EBOV) historically is the most lethal, with its sporadic outbreaks resulting in a CFR ranging from 60% (Minkébé, Gabon 1994, Gueckedou 2014) to 90% (Kéllé, Congo 2003). This is in sharp contrast to Reston ebolavirus (RESTV) which, despite its translational similarity to EBOV and serologic evidence of human transmission, has yet to result in even minor symptoms of the disease.

The viral protein, VP35, has been shown to be a multifunctional virulence factor by antagonizing anti-viral signalling pathways via its interferon inhibitory domain (IID). However, it is unlikely the VP35 pathways could fully account for the observed differential virulence between the species. Viral encoded miRNAs have already been identified in many species and shown to modulate the expression and antiviral function of interferons (IFNs).

This is the first paper to summarize the computational identification of a likely miRNA, termed the Pandora Element, within the intergenic, untranslated region of the Zaire ebolavirus nucleoprotein gene that appears to target multiple human transcripts. A structural characteristic of the RESTV Pandora domain will also be introduced that may also account for its differential virulence.

ABSTRACT The Ebolavirus outbreak of 2014 in West Africa is unprecedented. As of the most recent situation report from the World Health Organization on November 11, 2014, there have been 14,098 suspected, probable and confirmed cases with 5160 deaths reported globally in this Public Health Emergency of International Concern. 5 cases outside the continent of Africa have been reported. Entry and exit screening for EVD (Ebola Virus Disease) of individuals originating from known outbreak regions currently include the presence of fever or additional symptoms consistent with EVD. Despite these efforts, the rate of transmission [R(t)] remains at 1.4 to 1.7, transnational cases are increasing, and a resurgence of the outbreak in Mali has recently been reported. This perspective article discusses the pitfalls associated with the determination of fever in the screening process as well as the difficulties with individual, subjective self-reporting of symptoms.

THE GLYCOPROTEIN MUCIN-LIKE DOMAIN (MLD) IN THEZAIRE EBOLAVIRUS (EBOV) MAY BE RESPONSIBLE FOR THEMANIFESTATIONS OF POST-EBOLA VIRUS DISEASESYNDROME (PEVDS)

January 18, 2016

To study the mucin-like domain further, a comparative multi-sequence amino acid analysis of the poorly conserved MLD was performed and all 16 B-cell epitopes previously identified comparing all virulent species of Ebolavirus against RESTV was used to identify regions that could explain the differential virulence and vascular access to regions of immune privileged regions. Within the E1 epitope (301-316) of the MLD, the charged motif R (X1) EELSF demonstrated significant homology (86%) within the MHC Class II predicted epitopes did identify a statistically significant difference between the virulent species and RESTV. Three epitopes of acceptable binding affinities in the virulent group were significantly different from RESTV (p>.05) This study suggests that the residues located within the B-cell E1 epitope (301-316) and three MHC Class II epitopes may be responsible for vascular access to these immune privileged site and persistent symptoms observed in the convalescent PEVDS. Further studies are required into the potential role of VP40 in viral persistence and reemergence within these immune privileged areas; therefore potentially provide a therapeutic strategy in PEVDS and viral persistence associated with reemergence. virulent species but poorly conserved in RESTV (25%). In E5-E8, charged tandem grouping of charged residues in the motif Glu-336, Asp-337, and His-338 of EBOV were conserved as to charge in the virulent group but these charged residues were replaced by the uncharged Pro-336, Thr- 337, and Arg-338 in the RESTV sequence. The C-terminus GLINT motif in epitope E16 of the MLD at the GP2 junction was moderately conserved between all species including RESTV and therefore not felt to contribute to the overall differential virulence.

THE ZIKA VIRUS SFRNA SECONDARY STRUCTURE REVEALS A MIR-147A HOMOLOGUE THAT TARGETS 1 NEUROFASCIN AS A POTENTIAL CAUSE OF ITS NEUROLOGIC SYNDROMES

March 21, 2016

Pathologies associated with Zika virus infection include partial progressive paralysis (Guillan Barre Syndrome) and microcephaly in Brazil and Panama. We identified an 85 nucleotide stem loop structure in the 3' end of Zika virus sfRNA (position (343-428) with the canonical structural and sequence characteristics of a miRNA. In comparison, the West Nile Virus has been previously demonstrated to contain a miRNA in its 3’ untranslated (UTR) sfRNA region. The West Nile Virus miRNA, KUN-mir-1, was found to be 81 nucleotides in length (492-573) and 58% conserved overall as to the corresponding Zika virus stem loop nucleotide sequence. The majority on the sequence homology was in the terminal loop (78%). The 40 nucleotide (nt) 3p arm demonstrated 60% homology, decreasing at the distal segment. The 5p arm demonstrates on 42% sequence homology. The Zika virus stem loop in this study was identified to contain a hairpin structure in the 3’ end of the Zika virus sfRNA 3’ UTR segment predicted to contain a miRNA with significant homology to human hsa-mir-147a. Target analysis identified 241 human transcripts which include, but not limited to, neurofascin, synaptic vesicle glycoprotein 2A, neurofibromin 1, SAM and SH3 domain containing 1, neurogenin 2, in addition to multiple immune transcripts. Autoantibodies to neurofascin have been reported in in Guillan-Barre Syndrome (GBS), but have not yet been reported in or after Zika virus infection. A significant 9 mer match exists between the Zika virus miRNA 3p arm and the Neurofascin 3’UTR seed region, CCACACA. In contrast to West Nile Virus, GATA4 was not predicted to be, nor was identified in the MirBaseDB, to be a target of the Zika virus miRNA. These computational results indicate highly plausible mechanisms explaining the neurologic syndromes such a Guillan-Barre Syndrome and microcephaly associated with Zika virus infection, and warrant further investigation.

ZIKA VIRUS INDUCED NEUROTROPIC BRAIN INJURY:LESSONS FOR THE STUDY OF DISEASE ETIOLOGY ANDVACCINE DEVELOPMENT AGAINST PATHOGENS

April 7, 2016

Studies have found convincing evidence of association of ZIKV with Guillan-Barre Syndrome (GBS), a small preliminary report suggests association with microcephaly in one location. We have previously found a plausible cause (molecular mimicry to Polio Virus Receptors A, B and C). We also found plausible evidence of pathways from ZIKV infection to microcephaly though P53-BAX-mitochondrial mediated apoptosis via the ZIKV capsid protein and the Helicase domain within the NS3 protein. A study of ZIKV infection in neural precursor cells found that infection hampered growth rates (Tang et al., 2016). To date, no specific mechanism of gestational microcephaly has been demonstrated. Here, we expand the list of plausible mechanisms of microcephaly in ZIKV. In fact, ZIKV appears to be a potential “perfect storm” candidate for microcephaly. We conclude with open questions and future directions.

THE PROLAPSED INTERVERTEBRAL DISC THE HIGH-INTENSITY ZONE WITH DISCOGRAPHY CORRELATION

January 1997

Study Design: The study compared the presence of the high-intensity zone on magnetic resonance imaging with the results of awake discography. Objectives: To see if there was a correlation between the results of awake discography and the presence of a high-intensity zone on magnetic resonance imaging. Summary of Background Data: The evaluation of discogenic pain has proved to be somewhat elusive. Recent studies have indicated the high-intensity zone as being highly sensitive in the diagnosis of the painful discogenic segment. The present study was designed to investigate whether the presence of a high-intensity zone is associated with a concordant pain response on awake discography.

FDA regulations require safety testing of constituent ingredients in drugs (21 CFR 610.15). With the exception ofextraneous proteins, no component safety testing is required for vaccines or vaccine schedules. The dosing ofaluminum in vaccines is based on the production of antibody titers, not safety science. Here we estimate aPediatric Dose Limit that considers body weight. We identify several serious historical missteps in past analysesof provisional safe levels of aluminum in vaccines, and provide updates relevant to infant aluminum exposure inthe pediatric schedule considering pediatric body weight. When aluminum doses are estimated from FederalRegulatory Code given body weight, exposure from the current vaccine schedule are found to exceed our estimateof a weight-corrected Pediatric Dose Limit. Our calculations show that the levels of aluminum suggested bythe World Health Organization place infants at risk of acute, repeated, and possibly chronic exposures of toxiclevels of aluminum in modern vaccine schedules. Individual adult exposures are on par with ProvisionalTolerable Weekly Intake “limits”, but some individuals may be aluminum intolerant due to genetics or previousexposures. Vaccination in neonates and low birth-weight infants must be re-assessed; other implications for theuse of aluminum-containing vaccines, and additional limitations in our understanding of neurotoxicity andsafety levels of aluminum in biologics are discussed.

When the dorsal root ganglion is irritated by any of a variety of mechanisms, pain is referred to the various structures innervated by that root. In many circumstances, this pain is specific and may be used as a diagnostic aid. Unfortunately, emphasis is placed on defining a dermatomal distribution; the existence of a myotomal or sclerotomal origin of re­ferred pain is often overlooked. This review pre­sents the embryologic, anatomic, and neurophysio­logic etiology of referred pain from the lumbar spine.Low back pain is one of the most common presentations to the orthopedic surgeon, af­fecting nearly 85% of the population during their lifetime. It is frequently accompanied by radiation and/or dysesthesias down the length of one or both of the lower extremities in ei­ther a dermatomal,1, 2 or somatotopic (scleroto­mal3,7 or myotomal8) sensory pattern. Additionally, moderate to acutely tender distal motor points have been described in disk pathology.8, 9“Referred pain” is defined as pain that is felt in a region other than its source of origin.10 For example, pain from myocardial ischemia is commonly referred to the left arm, that from splenic abnormalities to the left shoulder, and that from an' acutely inflamed appendix to the umbilicus11. As with visceral structures, when a spinal nerve root ganglion is irritated pain, is referred to the various structures innervated by that root. In many circumstances, this pain is specific and may be used as a diagnostic tool. Unfortunately, emphasis is placed on defining a dermatomal distribution, and little emphasis is attributed to the existence of the myotome or sclerotome.The purpose of this review is to recapitulate the embryologic basis for referred pain pat­terns, with specific regard to their dermato­mal, myotomal, and sclerotomal origin. In ad­dition, we present the current understanding of the neurophysiologic and anatomic basis of referred pain of lumbosacral origin.

CHAPTER FIVE - DIAGNOSIS AND DRUG RESISTANCE OF HUMAN SOIL-TRANSMITTED HELMINTH INFECTIONS: A PUBLIC HEALTH PERSPECTIVE

January 25, 2025

Soil-Transmitted Helminths (STH) infections represent a major public health problem in developing countries. Ascaris lumbricoides, Trichuris trichiura, Hookworm and Strongyloides stercoralis are the four most important STH. They make up the biggest burden of disease among helminth infections and are classified as neglected tropical diseases (NTD). These four parasitic helminths afflict some of the most socio-economically disadvantaged groups worldwide. Currently, there is no, universally accepted ‘gold standard’ diagnostic method recommended for STH infections. The Kato-Katz [1] technique is recommended by the World Health Organization (WHO) for monitoring large-scale treatment programs to control morbidity due to STH, however it is not suitable to screen for S. stercoralis. Monitoring and evaluation during mass drug administration (MDA) programs faces two challenges. First, there is a need for diagnostic tests with improved sensitivity to enable detection of low-intensity helminth infections for all species including S. stercoralis. Second, a ‘susceptibility profile alert’ for the emergence of parasite drug resistance is imperative. To overcome these two challenges novel molecular tests need to be developed and the mechanisms of resistance have to be further investigated. Currently combinations of two or more tests are required to make a complete diagnosis of all STH species. Sensitivity problems for STH detection can be overcome with real-time PCR (qPCR), like a multiplex qPCR. Tests with great sensitivity are needed in the post-elimination phase. Future perspective should examine cost effectiveness of STH diagnostic tools to improve control and prevention strategies based in the diverse realities of each region: Asia, Africa, Oceania and America. Our review examines direct, indirect, molecular and alternative techniques for STH in the different strategy stages of diagnosis and control programs, tools for drug resistance, low resources-settings and the best field applicability tests.

Filovirus (Ebolavirus, Marburgvirus, Cuevavirus) binds to receptors on the cell surface through the viral spike glycoprotein. Prior studies have demonstrated that the virus initially enters the host cells by using different uptake mechanisms including lipid raft, receptor mediated clathrin-dependent endocytosis and/or macropinocytosis [1,2].

After internalization of the virus following macropinocytosis into the endosomes of the host cell, proteolysis of the viral trimeric glycoprotein (GP1/GP2) by two cysteine proteases, CTSB/cathepsin B and CTSL/cathepsin L, further induce a conformational change of GP2. This allows its binding of the virus to the host entry endosome receptor NPC1 at its loop 2 domain C site. This unmasks the filovirus GP2 fusion peptide to initiate fusion with the endosome membrane [3] which results from proteolytic cleavage of GP1 by the endosomal proteases cathepsin B and cathepsin L [4].

The binding of the viral glycoprotein (GP) to the host endosomal NPC1 appears to be position specific. Ng et al [5] identified a critical aspartic acid residue (Asp502) in domain C of loop 2 (371-615) of NPC1 which, when substituted by Phe502, significantly diminished infectivity within the African straw-colored fruit bats (Eidolon helvum). Hoffman et al [6] also identified variable infectivity with the straw-colored fruit bat and concluded that filoviruses rely on the same host cell factors for entry into human and fruit bat cells, although the efficiency of the usage of these factors might differ between filovirus species via the interactome with bat NPC1 loop 2.

Data:

The NPC1 DDFF Motif is Conserved Across Multiple Species

Our BLASTp alignment identified 41 of 159 (25%) unique species with the conserved DDFF motif in NPC1 loop 2. 54 species were identified (34%) with the conserved tandem DD residues within the DDFF motif. The alignment also appeared to demonstrate significant covariance with a substitution of Asp502->Glu502 (n=62) that may or may not have significant effect on infectivity. Further studies remain to be studied as to the effect of that covariant nonsynonymous substitution on filovirus infectivity.

Ebola Glycoprotein/NPC1 Interactive Model

PDB file 5JNX (Ebola Zaire) was obtained from the protein databank and visualized with UCSF Chimera. Chain E (EBOV GP2) was isolated along with Chain A|NPC1 loop 1 (1-316) and loop 2 (317-615)-[Image 1]. We identified 15 residues in EBOV GP2 that interacted with NPC1 [Image 3]. 14 interactions were with loop 2 and a single surface interaction was identified between GP2 (Tyr137) and loop 1 of NPC1 (Gly178).The Lys84 in GP2 formed extensive electrostatic interactions with the tandem aspartic acid residues (Asp501-Asp502) in NPC1 in addition to Gln421.

We also show the Asp502 residue is located within a highly conserved DDFF motif of the host NPC1 loop 2 Domain C. Asp502 in host NPC1 appears to form significant Van der Waals surface interactions with the Ebolavirus Phe88, Gly89, and Trp86 facing residues. Possibly more significantly, our computational modeling demonstrates extensive electrostatic interactions with the Ebola GP Lys84 residue within loop 2. This interaction is also shared with the adjacent Asp501 residue which very likely may further enhance the binding capacity. NPC1 Asp501 also appears to form a single hydrogen bond with the Ebola GP Thr83 residue. The host target NPC1 Phe503 residue appears to form primarily Van der Waals surface interactions with Ebola Gly87 and Trp88. NPC1 Phe504 appears to have only a minor surface interaction with Ebola GP Ser142. It would therefore appear that the tandem Asp-Asp residues (Asp501->Asp502) within the DDFF motif of NPC1 loop 2, domain C, form the greatest contribution to the binding between filovirus GP and host NPC1 and are critical to infectivity. Our study also suggests that a substitution of Lys84 within the Ebola GP interactome mat also have a significant effect on binding capacity due to its extensive electrostatic interaction with the NPC1 tandem Aspartic acid residues at positions 501-502.

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NPC1 alignment

Our BLASTp alignment identified 41 of 159 (25%) unique species with the conserved DDFF motif in NPC1 loop 2. 54 species were identified (34%) with the conserved tandem DD residues within the DDFF motif. The alignment also appeared to demonstrate significant covariance with a substitution of Asp502->Glu502 (n=62) that may or may not have significant effect on infectivity. Further studies remain to be studied as to the effect of that covariant nonsynonymous substitution on filovirus infectivity.

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Filovirus SsGP Alignment

Representative small-secreted GP sequences for EBOV, SUDV, BDBV, TAFV, RESTV, MARV, RAVN, and LLOV were obtained by BLASTp using EBOV as the query at NCBI and aligned using Clustal Omega in Jalview. Interacting residues identified in the model were marked for identification and conservation across species. Lys84 was 100% conserved across all species of filovirus.

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Summary

From prior published reports, this modeling exercise would support the conclusion by Ng et al that the host DDFF motif in the filovirus receptor NPC1 containing Asp502 is a factor with infectivity. The extensive electrostatic interactions between the GP2 Lys84 and NPC1 (Asp501-Asp502, Gln421) would support Hoffman et al that an Ebolavirus species specific substitution of Lys84 would very likely effect infectivity even if the tandem Asp residues (Asp501-Asp502) were conserved in target NPC1. It must be mentioned that the Lys84 residue is 100% conserved across all species of Filoviridae further suggesting either host NPC1 molecular interacting residues or other interacting residues besides the tandem aspartic acid residues play a more significant role in infectivity.

RESEARCH OUTLOOK: COMPLEX SYSTEMS

January 25, 2025

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